26 Indian Journal of Agricultural Sciences 81 (12): 1116–23, December 2011 Comparative assessment of microsatellite and RAPD markers and their efficiency in DNA fingerprinting of upland cotton (Gossypium hirsutum) VIJAY N WAGHMARE 1 , S R SUTAR 2 , P B THAKRE 3 , D R SAPKAL 4 , R V SALAME 5 , A M BADOLE 6 and B R PATIL 7 Central Institute for Cotton Research, Nagpur, Maharashtra 440 010 Received: 18 May 2010; Revised accepted: 22 September 2011 ABSTRACT A statistical approach was employed to compare the potential of microsatellite (SSR) and RAPD markers for identification, diversity analysis and genotype discrimination. Twentyfour SSR and seventeen RAPD primers were screened across 91 upland cotton (50 maintainer and 41 restorers) accessions. Major parameters, i e polymorphism information content (PIC), resolving power (Rp) and marker index (MI), were computed and compared for their ability to discriminate among the accessions. PIC, Rp and MI values displayed wide variation among SSR and RAPD markers. MI values showed excellent linear relationship with number of genotypes identified (r 2 = 0.70 and 0.69) by SSR and RAPD markers than Rp (r 2 = 0.63, 0.56). SSR and RAPD markers selected based on informative PIC, high Rp and MI values independently discriminate majority of accessions. However, combined use of SSR and RAPD markers, increases the efficiency and discrimination power. Minimum of 8 markers (4 SSR and 4 RAPD) possessing high MI and Rp values were found to discriminate as many as 90 out of 91 accessions. This study reveals that selection of markers based on Rp and MI values for DNA fingerprinting and diversity studies was highly reliable and such selective markers could be effectively used for characterization of large germplasm accessions. Key words: DNA fingerprinting, Gossypium, Marker index, Polymorphism information content, Resolving power, Upland cotton DNA fingerprinting is an important tool for characterization of germplasm and establishment of identity of varieties/ hybrids/ parental genotypes in plant breeding and germplasm management. For protecting proprietary germplasm, molecular markers have played an important role in securing plant variety rights by virtue of their unique efficiency in distinguishing even the closely related germplasm accessions. Several PCR-based marker have been developed in last two decades. The random amplified polymorphic DNA (RAPD) has been used for genotype identification in several crops plants (Dongre and Kharbikar 2004, McGregor et al. 2000, Mondal et al. 2008, Rana and Bhat 2004). Simple sequence repeat (SSR) markers are potentially powerful for DNA fingerprinting and have widespread application in plant genome analysis (Morgante and Olivieri 1993). The availability and abundance of microsatellite (or SSR) markers throughout the cotton genome and the fact that they are polymorphic, codominant and are polymerase chain reaction (PCR)-based, make them particularly useful in genetic diversity studies in cotton (Reddy et al. 2001). Microsatellite markers have been used for DNA fingerprinting by several researchers (Belaj et al. Cotton (Gossypium hirsutum L.) is the world leading natural fibre crop. Cotton belongs to genus Gossypium and it comprises 45 diploid and five allotetraploid species that occur naturally through the semi-arid and arid region of Africa, Australia, Central and South Africa, the Indian sub- continent, Arabia, Galapagoes, and Hawaii (Fryxell 1979). During the course of evolution, four species whose seed fibres were long and spinnable were domesticated. India maintains second largest germplasm bank of all four cultivated cotton species with total of about 9954 accessions at Central Institute for Cotton Research, Nagpur. Conservation and management of such huge accessions is a challengeable task and requires reliable means of genotype/cultivar identification that can be applied routinely to large number of accessions. 1 Senior Scientist (e mail: vijayvnw@yahoo.com), 2 Senior Research Fellow (e mail: satyam111222@yahoo.co.in), 3 Senior Research Fellow (e mail: prajwal_002@rediffmail.com), 5 Technical Officer (e mail: rvsalame@gmail.com), 6 Technitian (e mail: badoleam@rediffmail.com), Division of Crop Improvement 4 PhD Student (e mail: deepaksapkal7878@rediffmail.com), 7 Senior Cotton Breeder (e mail; brpcotton@ Dr Punjabrao Deshmukh Krishi Vidyapeeth, Akola